[English] 日本語
Yorodumi
- EMDB-46868: Streptococcus pneumoniae GAPN with NADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46868
TitleStreptococcus pneumoniae GAPN with NADP
Map data
Sample
  • Complex: GAPN with NADP+
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase
KeywordsGAPN / NADP / OXIDOREDUCTASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsEunjeong L / Elan ZE
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Biochemical, structural, and biologial studies of Streptococcus pneumoniae GapN reveal a key metabolic player necessary for host infection.
Authors: Eunjeong L / Elan ZE
History
DepositionSep 4, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46868.png

Downloads & links

-
Map

FileDownload / File: emd_46868.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 256 pix.
= 201.728 Å		0.79 Å/pix.
x 256 pix.
= 201.728 Å		0.79 Å/pix.
x 256 pix.
= 201.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.83469474 - 1.2069149
Average (Standard dev.)0.00039249868 (±0.05010124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 201.728 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_46868_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_46868_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GAPN with NADP+

EntireName: GAPN with NADP+
Components
  • Complex: GAPN with NADP+
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenase

-
Supramolecule #1: GAPN with NADP+

SupramoleculeName: GAPN with NADP+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pneumoniae (bacteria)

-
Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase

MacromoleculeName: Glyceraldehyde-3-phosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTRYQNLVNG KWKSSEQEIT IYSPINQEEL GTVPAMTQTE ADEAMQAARA ALPAWRALSA IERAAYLHKT AAILERDKEK IGTILAKEVA KGIKAAIGEV VRTADLIRYA AEEGLRITGQ AMEGGGFEAA SKNKLAVVRR EPVGIVLAIA PFNYPVNLSA SKIAPALIAG ...String:
MTRYQNLVNG KWKSSEQEIT IYSPINQEEL GTVPAMTQTE ADEAMQAARA ALPAWRALSA IERAAYLHKT AAILERDKEK IGTILAKEVA KGIKAAIGEV VRTADLIRYA AEEGLRITGQ AMEGGGFEAA SKNKLAVVRR EPVGIVLAIA PFNYPVNLSA SKIAPALIAG NVVMLKPPTQ GSISGLLLAK AFEEAGIPAG VFNTITGRGS EIGDYIIEHK EVNFINFTGS TPIGERIGRL AGMRPIMLEL GGKDAALVLE DADLEHAAKQ IVAGAFSYSG QRCTAIKRVI VLESVADKLA TLLQEEVSKL TVGDPFDNAD ITPVIDNASA DFIWGLIEDA QEKEAQALTP IKREGNLLWP VLFDQVTKDM KVAWEEPFGP VLPIIRVASV EEAIAFANES EFGLQSSVFT NDFKKAFEIA EKLEVGTVHI NNKTQRGPDN FPFLGVKGSG AGVQGIKYSI EAMTNVKSIV FDVK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: OTHER / Number images used: 1068956
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more